Science needs more research software engineers • Hacker News Board

Re: Science needs more research software engineers

#331

Post by [deleted] » Wed, Jun 01, 2022, 11:54 PM UTC

joshvm wrote: post #101

Azrael3000 wrote: post #54

Earlier quoted context omitted.

There is simply no incentive for science to do proper software engineering. It does not directly produce papers or money, so nobody does it. I've seen it several times in my own career in several countries. PhDs having their own version of the code, incompatible with the one of the Postdoc sitting opposite of them. Each slaving away at their niche project but nobody there to bring it all together. This particular uni…

RSEs should not be working on, or assisting, research at the PhD level. By that I mean news/skunkworks stuff. They should be taking the output from a PhD and turning it into core software for the group. That doesn't solve the collaboration issue between PhDs/Postdocs, but there is a particular point in a research project lifecycle where it makes sense to hire an RSE. A bigger challenge is that most PIs are not projec…

[deleted]

Re: Science needs more research software engineers

#332

Post by DrewADesign » Thu, Jun 02, 2022, 12:14 AM UTC

908B64B197 wrote: post #320

DrewADesign wrote: post #168

Earlier quoted context omitted.

It certainly echoes my experience having just left a professional dev job in academia after an 11 year stretch. Anybody without academic credentials relevant to the subject matter is "the help" no matter how much you contribute, and it's flat-out demoralizing. I worked on a tech-heavy project large enough to get an NYT feature article covering its launch. For it, I collaborated heavily on the service design and logis…

> Anybody without academic credentials relevant to the subject matter is "the help" no matter how much you contribute, and it's flat-out demoralizing. That's my number one advice regarding academia: unless there's a path toward a valuable visa, or it's paid work while getting a valuable degree (read, something that will have the prestige to open doors) or your co-author at a good university you're much better buildin…

This is different, though. I was a professional developer working in a non-academic lab doing work the academic world really cared about. Public recognition for big accomplishments is what distinguishes me from the 'web guy' at the help desk who knows how to customize Wordpress themes, and will lead to progressively interesting roles that pay well in exciting organizations. Just having X number of publications under my belt wouldn't budge the needle for my career. It's a weird sort of in-between spot without obvious career trajectories but you can get a decent salary while working on cool stuff.

Re: Science needs more research software engineers

#333

Post by DrewADesign » Thu, Jun 02, 2022, 12:18 AM UTC

linuxftw wrote: post #284

DrewADesign wrote: post #168

Earlier quoted context omitted.

It certainly echoes my experience having just left a professional dev job in academia after an 11 year stretch. Anybody without academic credentials relevant to the subject matter is "the help" no matter how much you contribute, and it's flat-out demoralizing. I worked on a tech-heavy project large enough to get an NYT feature article covering its launch. For it, I collaborated heavily on the service design and logis…

What you did doesn't matter, and they gave you the right amount of recognition. There are 1000's of imported indentured servants that will happily do your job the moment you leave. Of course, we don't call them indentured servants any more, we use terms like 'academic visa' or such. I'm sure they also didn't think the electricity company for keeping the lights on, or Microsoft for creating Windows to write their spee…

Nothing anybody does matters. It's all a big scam, man. ::hits birthday cake flavored vape and sips energy drink:: I'm looking out for number one from now on, bro.

Re: Science needs more research software engineers

#334

Post by photochemsyn » Thu, Jun 02, 2022, 12:32 AM UTC

jollybean wrote: post #323

photochemsyn wrote: post #306

Earlier quoted context omitted.

Fundamental: the patents produced by taxpayer-financed academic research have no business being exclusively licensed to some pharmaceutical corporation. As far as the cost of clinical trials being borne by those companies, well, let's get the FDA involved in the clinical trials. Then the competition can come in, i.e. whoever can produce pure preparations of those drugs at the lowest cost will win the most market shar…

No, if a Uni has developed some patents, and wants to 'exclusively license' them to a Pharma, that's probably a good application of that patent, they become much less worthwhile otherwise. It's a misunderstanding of the market to suggest that somehow 'the FDA will lead the trials'. This is about as likely as a manned mission to Venus, it won't happen, and it shouldn't happen for good reason (cost vastly outweighs the…

Non-exclusive licensing is the far better option. This prevents monopolization and ridiculous price increases. As far as clinical trials by exclusive license holders, those have a rather poor record of producing reliable results over the long term in many cases (Vioxx of course, there are many others). The trials should really be independently run, not controlled by the very corporations that have a vested interest in seeing positive results so they can go to market.

As far as Covid-19 vaccines, there are actually many companies ready to go right to production if those patents are released to the public at this moment, and that would greatly increase supply, and that would benefit the whole world, instead of a handful of pharma CEOs and affiliated shareholders.

Re: Science needs more research software engineers

#335

Post by kongolongo » Thu, Jun 02, 2022, 1:38 AM UTC

photochemsyn wrote: post #306

kongolongo wrote: post #234

Earlier quoted context omitted.

I think this is only a half-truth. There certainly are examples of academic research being translated into lucrative products by industry (there are even prominent examples in software/systems engineering) but I think that many times the translation of academic research into a useable product is also a massive endeavor that deserves recognition in its own right. I see this scenario described in medical research all t…

Fundamental: the patents produced by taxpayer-financed academic research have no business being exclusively licensed to some pharmaceutical corporation. As far as the cost of clinical trials being borne by those companies, well, let's get the FDA involved in the clinical trials. Then the competition can come in, i.e. whoever can produce pure preparations of those drugs at the lowest cost will win the most market shar…

>manufacturing platforms (much of this is now outsourced to India, Mexico, etc. for drugs being sold in the USA)

This completely trivializes and misses the fact that the manufacturing process itself can be patented.

>As a practical example, look how the best Covid vaccines (mRNA types) have been monopolized, leading to low rates of vaccination in Africa etc., even though that was technology developed with taxpayer funding at public universities.

That's just patently false, Moderna for example, has been waived patent infringement related to covid vaccines. The reason the developing world does not have high rates of vaccination is not because of patents but primarily because of their infrastructure.

Re: Science needs more research software engineers

#336

Post by kongolongo » Thu, Jun 02, 2022, 1:40 AM UTC

photochemsyn wrote: post #334

jollybean wrote: post #323

Earlier quoted context omitted.

No, if a Uni has developed some patents, and wants to 'exclusively license' them to a Pharma, that's probably a good application of that patent, they become much less worthwhile otherwise. It's a misunderstanding of the market to suggest that somehow 'the FDA will lead the trials'. This is about as likely as a manned mission to Venus, it won't happen, and it shouldn't happen for good reason (cost vastly outweighs the…

Non-exclusive licensing is the far better option. This prevents monopolization and ridiculous price increases. As far as clinical trials by exclusive license holders, those have a rather poor record of producing reliable results over the long term in many cases (Vioxx of course, there are many others). The trials should really be independently run, not controlled by the very corporations that have a vested interest i…

>As far as Covid-19 vaccines, there are actually many companies ready to go right to production if those patents are released to the public at this moment, and that would greatly increase supply, and that would benefit the whole world, instead of a handful of pharma CEOs and affiliated shareholders.

That's just conspiracy. Many companies have not been enforcing any patents related to covid vaccines. The reason why the developing world does not have high vaccine adoption is because of their infrastructure, not because of patent blocking.

Re: Science needs more research software engineers

#337

Post by myst1 » Thu, Jun 02, 2022, 2:38 AM UTC

aqsalose wrote: post #294

coastflow wrote: post #276

Earlier quoted context omitted.

>"I bet a third of them once were physical scientists/mathematicians who mostly regret their degrees" Would mathematicians truly be regretting their degrees, if they decide to work in software? I read that mathematics one of the best degrees for a career in software engineering, as computer science is very closely related to mathematics (to the point where studies of algorithms are largely the same for mathematics an…

Theoretical parts of computer science is connected to discrete mathematics, sure. But that is only a subfield of mathematics and mostly happens already at CS departments, so you'd get a CS degree anyway. It is also possible that aptitude for math is related to aptitude in software engineering. However: The mathematics content of 90%+ of mathematics degrees awarded is fully irrelevant to 95%+ of software development t…

And five years of gluing APIs together that help get more people to click advertisements - you'd be surprised how much math you forget. Machine learning can be better for exercising math, but most company's do not want anyone doing anything new. Same goes for physical sciences in my experience. You basically get a PhD to do associates level work. Even if you know a better way, that comes after you get ten yrs experience and have authority over projects. See the first sentence of this post for a catch 22. Bleh.

Re: Science needs more research software engineers

#338

Post by peterhalburt33 » Thu, Jun 02, 2022, 3:01 AM UTC

rob_c wrote: post #152

throwmamatrain wrote: post #60

This looks great, and I would have loved to see this when I was in the lab. When the software industry says to you: "We will nearly triple your salary, you don't have to work weekends, and you also don't have to feed the mice on a Sunday night." You will 100% take this deal. I was a 10yr+ academic tool maker in biochemistry, built cutting edge microscopes, hardware, and image analysis software. My lab was successful…

> at least in bioscience... BINGO! that field is notoriously horrible and interacts extremely badly with a 'when not discovered here, not important' syndrome. Biology is brutal toward bio-physicists, mathematicians as well as people who code who they are forced to work with rather than seek out to help them. I still hold up as an example nonsense discussions around p-values in bio vs actual work going on in statistic…

I will say IMO (and experience) in professional math that while there is perhaps more of a chance for an outsider to have an impact, Mathematics is hardly free from bias towards insiders: it can manifest itself as subtly as using notation as a shibboleth (e.g. it’s somewhat easy to tell which community an author comes from through their notation and terminology, and equally easy to harbor resentment towards those outside your field) all the way to active “prove I’m the most clever in the room” syndrome during seminars. I’d like to think that a more collaborative atmosphere is prevailing now due to the rise of interdisciplinary and applied math, but people are people everywhere and as Sayre stated “Academic politics is the most vicious and bitter form of politics, because the stakes are so low.”

Re: Science needs more research software engineers

#339

Post by zach_garwood » Thu, Jun 02, 2022, 3:31 AM UTC

cycomanic wrote: post #258

joshuaissac wrote: post #178

Earlier quoted context omitted.

> Should they pay the software engineer more than everyone else, even though they don't even work on the core mission (i.e. the science)? They do not have to pay the software engineer anything if they can find one who is happy with getting nothing. Salary is always going to be a factor in who they can attract, especially when their competitors can offer much better compensation. If they are satisfied with the softwar…

But that's my point, the software developer is not a crucial role in the research process (unlike (most) professors arguably), they are nice to have and definitely helpful, but getting a grant to do research is difficult enough, paying all the funds to a software developer means no research gets done. In other words in most cases a software developer does not add enough value to justify their cost if they get paid li…

If the developers don't play a crucial role, then why did I just read an article claiming we need more of them?

Re: Science needs more research software engineers

#340

Post by peterhalburt33 » Thu, Jun 02, 2022, 4:00 AM UTC

pyb wrote: post #117

kergonath wrote: post #96

Earlier quoted context omitted.

Yeah. Considering how much time we spend developing and using the damn things, we’ll call them the way we like, thank you very much. We don’t really need condescending software types to just come and explain to us how we’re saying it wrong. That is particularly rich, considering the tendency of CS people to cargo cult and borrow physical terms without understanding them.

Always annoying to hear machine learning people speak of "tensors"...

It aggravates me too, however, considering that the definition of a tensor according to mathematicians is an element of the tensor product of two vector spaces (or whatever other objects you can tensor together), and according to physicists would be an object which transforms like a tensor, I’m somewhat sympathetic. Neither definition sheds any light on what a tensor is to anyone who doesn’t already understand what a tensor is, and I’m convinced that the moment one understands what tensors are they lose the ability to explain what tensors are.